Genome Evolution of Influenza Virus
Influenza Overview General The influenza virus is responsible for various deadly pandemics throughout history as well as endemic outbreaks responsible for the flu in 5-20% of people in the United States each year. The influenza virus is a member of a family of viruses named Orthomyxoviridae and is characterized by 8 negative single stranded RNA genome segments (1). Symptoms The symptoms associated with the flu are comparable to those of the common cold but on a much more severe scale. These symptoms include fever, chills, muscle aches and pains, sore throat, coughing, general discomfort and weakness, fatigue, and headache (1). Other possible symptoms can include vomiting and general nausea. Generally these symptoms last about 1-2 weeks and have a greater likelihood of lasting/occuring in the elderly, young, and immunocompromised individuals (1). Transmission The flu can be spread during the viral incubation period 1 day before symptoms appear up through approximately 5-7 days with present symptoms making the virus highly contagious (1). There are a multitude of different ways the virus can be spread which also contributes to its high level of transmission. Influenza virus can be spread by direct hand contact with an infected person and then touching areas containing mucus membranes such as eyes, mouth, or nose (1). A second transmission route the virus is spread is through aerosolized viral particles such as when an infected person sneezes or coughs and the particles are then inhaled by another uninfected individual. Thirdly the virus can be spread through touching a contaminated surface that contains live viral particles (1). Genome Evolution/ Variation Study Overview This study focused primarily on Influenza A virus strains and their associated mutation rates. Since the virus has such a high rate of mutation leading to novelty strains each year, predicting genome evolution in this virus is essential for coming up with an effective vaccine (2). Therefore the point of this study was to conduct a large scale sequence of the viral genome in order to help better identify evolution and transmission patterns (2). Approximately 209 genomes from different influenza A viruses were sequenced from this project. In order to help eliminate bias the influenza isolates were all obtained from a constrained geographical area and across the time period of several flu seasons (2). Materials and Methods The viral RNA isolated was first amplified in cultures of primary rhesus monkey kidney cells and th en extracted from the supernatant (2). The RNA was then treated and then exposed to T4 RNA ligase enzyme which circularized the RNA and RT-PCR was performed to amplify the sequences. The sequences were then read using Big Dye Terminator chemistry to obtain the final genome read for each of the viral particles (2). Results In total all 8 segments from 207 H3N2 isolates and 2 H1N2 isolates were completely sequenced (2). The 207 H3N2 sequences were aligned by organizing the genome sequence reads down into the 10 vital viral proteins (HA, NA, PB2, PB1, PA, NP, M1, M2, NS1, and NS2) as well as the chronological order of the seasons the viruses were obtained in. The image to the right demonstrates the vast mutation rate found within the viruses in the short time span of just a few years. Each row represents a single amino acid position within one protein. The variations in color across the row represents a different amino acid change found in at least 3 of the 207 isolates found. There are many important conclusions that come about as a result of these findings. One finding demostrates that certain mutations appear to be "selected for" by the virus. It can be presumed that these mutations aided in its replication and survival within the host. For example mutations found within certain segments of the PA, PB1, PB2, NP, NS1, NS2 first come about in the 2001-2002 season and remained consistently present afterwards in future seasons (2). There was also great evidence that indicated a reassortment event occured between genomes of two influenza virus particles. This was supported by the evidence that the virus isolates with dominant HA mutations during the 2003-2004 flu season had first arose in the viral genomes in Feb 2003. However the fact that mutations in other proteins that occured during this same time were minimally found in isolates from the 2003-2004 season indicates that a reassortment event was responsible for the new dominant HA segment during this time (2). Other important conclusions of this study indicated that certain HA mutations sequenced in this study may effect receptor-binding affinity and thus increase the viruses ability to replicate proficiently (2). For example, a mutation in HA at position S186G was present in viruses through out the 2001-2002 flu season and then remained present for the 2003-2004 flu season which is indicative that these mutation increased the viruses overall "fitness" level (2). References 1. "Influenza." Wikipedia. Wikimedia Foundation, 16 Nov. 2014. 2. Ghedin, Elodie. "Large-scale Sequencing of Human Influenza Reveals the Dynamic Nature of Viral Genome Evolution." Nature.com. Nature Publishing Group, 16 Sept. 2005.